BASIN: Bayesian mAtrix variate normal model with Spatial and sparsIty priors in Non-negative deconvolution

arXiv:2510.16130v2 Announce Type: replace
Abstract: Spatial transcriptomics allows researchers to visualize and analyze gene expression within the precise location of tissues or cells. It provides spatially resolved gene expression data but often lacks cellular resolution, necessitating cell type deconvolution to infer cellular composition at each spatial location. In this paper we propose BASIN for cell type deconvolution, which models deconvolution as a nonnegative matrix factorization (NMF) problem incorporating graph Laplacian prior. Rather than find a deterministic optima like other recent methods, we propose a matrix variate Bayesian NMF method with nonnegativity and sparsity priors, in which the variables are maintained in their matrix form to derive a more efficient matrix normal posterior. BASIN employs a Gibbs sampler to approximate the posterior distribution of cell type proportions and other parameters, offering a distribution of possible solutions, enhancing robustness and providing inherent uncertainty quantification. The performance of BASIN is evaluated on different spatial transcriptomics datasets and outperforms other deconvolution methods in terms of accuracy and efficiency. The results also show the effect of the incorporated priors and reflect a truncated matrix normal distribution as we expect.